The U.S. Supreme Court case Alaska Department of Environmental Conservation v. Environmental Protection Agency (2003) revolved around the EPA's authority to overrule state decisions regarding air pollution control under the Clean Air Act. The State of Alaska had granted permits for a company to increase its pollutant emissions, which was challenged by the EPA on grounds that it violated federal law and would harm public health or welfare. The State argued that only they had power to enforce such laws within their jurisdiction, not the federal agency. However, in a 5-4 decision, the Supreme Court ruled in favor of EPA stating that it indeed possessed authority under Section 167 of Clean Air Act to enforce prevention measures against significant deterioration of air quality even when a state has issued permit allowing increased emissions from new or modified major emitting facilities. This ruling affirmed that national environmental standards could override individual state decisions if they failed to adequately protect public health and environment.

In the dissenting opinion for Alaska Department of Environmental Conservation v. Environmental Protection Agency, Justice Clarence Thomas argued that the majority had overstepped its bounds by allowing the EPA to veto a state's decision under the Clean Air Act without clear congressional authorization. He contended that this interpretation was inconsistent with federalism principles and gave too much power to federal agencies at the expense of states' rights. Furthermore, he disagreed with how broadly his colleagues interpreted "best available control technology" (BACT), arguing it should not include cost-effectiveness considerations or potential alternatives outside a proposed project’s scope. In essence, Justice Thomas believed that in this case, EPA had exceeded its authority and intruded upon powers reserved for individual states.